I understand the idea of weaponless defenders in the early game, but what I think the OP was wondering about is why the AI would put defenses on those ships. I have frequently wondered at that myself. I see it especially from the Drath (who always seem to research a few levels of armor and/or shields before they develop any weapons tech).
A 0/1 defender is just as dead as a 0/0 defender if an enemy ship shows up and starts shooting. It's more expensive too.
On a similar note, why in the world do all of the troop transports get one free defense in each category? Again, if there is any ship alive to shoot at an unarmed transport, it is eventually going to die, regardless of any defense it has. I suppose it might help for armed transports based off hulls other than the 1 HP cargo hull, but by the time I have tech enough to consider that, the ships I would likely run into would not be bothered by a measly 3 defense.
Anyway, I'm really happy with the game, and always impressed to see the developers out herding cats in the forums.